R: Label 'propd' Pairs by DE Results

getColours {propr}

R Documentation

Label `propd` Pairs by DE Results

Description

The getColours function "colours" the pairs based on a vector of differential expression (DE) results. If both members in the pair are DE, the colour is "Green". If both members in the pair are not DE, the colour is "Red". If only one is DE, the colour is "Yellow". This allows the results of a DE analysis to affect the interpretation of differential proportionality. Importantly, the significance of differential proportionality is independent of the DE method used.

Usage

getColours(object, DE, cutoff = NA, include = NA, or = TRUE)

getColors(object, DE, cutoff = NA, include = NA, or = TRUE)

Arguments

`object`	Any `propd` object.
`DE`	A logical vector. The i-th element should state whether the i-th gene is differentially expressed.
`cutoff`	For `updateCutoffs`, a numeric vector. this argument provides the FDR cutoffs to test. For graph functions, a numeric scalar. This argument indicates the maximum theta to include in the figure. For graph functions, a large integer will instead retrieve the top N pairs as ranked by theta.
`include`	This argument indicates which features by name should belong to a pair for that pair to get included in the results. Subset performed by `Partner %in% subset \| Pair %in% subset`.
`or`	A boolean. If `FALSE`, `include` subsets by `Partner %in% subset & Pair %in% subset`.

Details

For use in conjunction with getNormTheta.

Value

A data.frame. The output of getResults with a "colour" column.